Cellranger

Introduction

Cellranger is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more. Detailed usage can be found here: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger.

Versions

  • 6.0.1

  • 6.1.1

  • 6.1.2

  • 7.0.0

  • 7.0.1

  • 7.1.0

Commands

  • cellranger mkfastq

  • cellranger count

  • cellranger aggr

  • cellranger reanalyze

  • cellranger multi

Module

You can load the modules by:

module load biocontainers
module load cellranger

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run cellranger our our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 20:00:00
#SBATCH -N 1
#SBATCH -n 48
#SBATCH --job-name=cellranger
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers cellranger

cellranger count --id=run_count_1kpbmcs --fastqs=pbmc_1k_v3_fastqs --sample=pbmc_1k_v3 --transcriptome=refdata-gex-GRCh38-2020-A